\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{graphicx}
\title{Automatically numbering compounds in chemical schemes}
%% Uncomment these lines if you get error about "too many \new..."
% \let\tmp\newinsert
% \let\newinsert\newbox
\usepackage{chemstyle}
% \let\newinsert\tmp
\usepackage{chemnum}
% For positioning the scheme captions at the top.
\floatsetup[scheme]{position=top}
\begin{document}
\begin{scheme}
%% hexa.eps has "TMP1" and "TMP2" as the markers
%% in fact EVERY .eps should start with TMP1, TMP2 etc
%% for ease of use
\replacecmpd{first:compound} %% automatically replace TMP1
\replacecmpd{second:compound} %% automatically replace TMP2
\includegraphics[width=\linewidth]{hexa}
\caption{This is something!}
\label{first:chem:scheme}
\end{scheme}
Compounds \refcmpd{first:compound} and \refcmpd{second:compound} in \ref{first:chem:scheme}. Here's a reference to in-text creation of \cmpd{RareCompound} that we can later refer to.
\vfill
\begin{scheme}
\replacecmpd{next:compound} %% automatically replace TMP1 BUT the autonumbering counter updates to 3!
\replacecmpd{last:compound} %% automatically replace TMP2
\includegraphics[width=\linewidth]{hexa}
\caption{This is something else!}
\label{second:chem:scheme}
\end{scheme}
Compounds \refcmpd{next:compound} and \refcmpd{last:compound} in \ref{second:chem:scheme}. Hey remember \cmpd{RareCompound}? \texttt{chemnum} still remembers it correctly, \emph{and} see how the compound numbering continues throughout the scheme diagrams!
\vfill
%% MANUAL UPDATING THE COMPOUND COUNTER; make sure you know what you're doing!
\setcounter{cmpdmain}{8}
\begin{scheme}
\replacecmpd{jumped:compound} %% automatically replace TMP1 BUT the autonumbering counter updates to 9!
\replacecmpd{nextjumped:compound} %% automatically replace TMP2
\includegraphics[width=\linewidth]{hexa}
\caption{This is again something else!}
\label{third:chem:scheme}
\end{scheme}
Compounds \refcmpd{jumped:compound} and \refcmpd{nextjumped:compound} in \ref{third:chem:scheme}. (Yes we manually modified the compound numbering counter after \ref{second:chem:scheme}).
\end{document}
